Expressed sequence tag databases | Transcription analysis
Expressed sequence tags (ESTs) are short DNA sequences (200–500 nucleotides) generated by sequencing the 5′ and/or 3′ ends of cDNAs that are subsequently clustered and counted (Adams et al., 1991). Source text: Feichtinger et al., 2014.
Provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB is a functional genomic database for Plasmodium spp. It belongs to a family of genomic resources that are housed under the EuPathDB Bioinformatics Resource Center (BRC) umbrella. Data in PlasmoDB can be queried by selecting the data of interest from a query grid or drop down menus. Various results can then be combined with each other on the query history page.
A database which offers gene annotation of cucurbit. This base offers the genome of Melon (Cucumis melo), Cucumber (Cucumis sativus), Watermelon (Citrullus lanatus), Pumpkin (Cucurbita maxima). The Cucurbitaceae consist of 98 proposed genera with 975 species, mainly in regions tropical and subtropical. All species are sensitive to frost. Most of the plants in this family are annual vines, but some are woody lianas, thorny shrubs, or trees (Dendrosicyos). Cucurbit belongs to the Cucurbitaceae family.
Provides a collection of short single-read transcript sequences. dbEST is a division of GenBank available as an online resource. This database includes sequence data and other information on single-pass cDNA sequences or expressed sequence tags (EST) from a number of organisms. The given sequences provide a resource to evaluate gene expression, find potential variation, and annotate genes.
Provides information about Trypanosomatidae. Tritrypdb is a collective database which intends to gather annotation, curation and access to tools enabling sophisticated queries against genomic scale datasets. Users can select more than 80 different searches against the TriTryp genomes and datasets and combine them in an integrated and graphical manner. All searches can be customized, summarized by species and displayed as an interactive gene list.
Gathers information concerning maternal gene expression information for Halocynthia roretzi. MAGEST is a database assisting in prediction of amino acid fragment sequences. This resource is dedicated to fragments of amino acid sequences that are predicted from the expressed sequence tag (EST) data sets.
Compiles information about Cryptosporidium. Cryptodb intends to collect whole genome sequence, annotation, sequence analysis and related data about this parasite. The database integrates a set of tools such as BLAST, a tool for annotate personal sequence or an interface for saving searching strategies. Searches can be made among nine data types including popset isolate sequences, single nucleotide polymorphisms (SNPs), open reading frames (ORFs), compounds or gene.
Provides an online resource of genomic data for key blood flukes (genus Schistosoma). SchistoDB integrates whole-genome sequence (WGS) and annotation of three species of the genus and provides enhanced bioinformatics analyses and data-mining tools. This database supplies access and visualization of the Schistosoma mansoni genome and features, integrated to other data types such as expressed sequence tags (ESTs), proteins and metabolic pathways.
Provides information about cDNA sequences. PEDE contains more than 68 000 high-quality expressed sequence tag (EST) collected from additional libraries. PEDE works with an Internet-based search interfaces. This database covers some porcine gene expression data. It enables scientists to prepare a catalog of genes likely to be of interest when pigs are used as animal models in research applications.
Compiles a set of protein expression and protein synthesis data added to human Gateway entry clones. HGPD compiles more than 40000 entry clones splitted in 10 protein function groups. The database allows users to make searches among the content which presents the open reading frames (ORFs) region of each cDNA. Moreover it includes in vivo cellular localization data of proteins for about 30000 humans Gateway entry clones.
Helps biologists to find the flanking insertion sites (FSTs) that interrupt the genes in which they are interested. The FLAGdb information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches. Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge.
Hosts several biological data for species in the Solanaceae and their close relatives, with data types ranging from chromosomes and genes to phenotypes and accessions. These data originate from a variety of sources including user submissions and data from other curated public databases. Moreover, in this database protein sequences are derived from protein predictions on both unigene transcript sequences and predicted genomic gene models.
A genomic database for Giardia lamblia. GiardiaDB is based on the genome of the WBC6 clinical isolate of G. lamblia. It is accessed via the standard EuPathDB web interface, providing a wide variety of tools for genomic database mining. In addition to BLAST and pattern/motif similarity searches, users can identify genes based on genomic position; common name or keyword; gene attributes (such as gene type, or number of exons); evidence of transcript expression including ESTs, SAGE tags, microarray and proteomics; gene product annotation (such as GO function, or EC enzyme number); and predicted cellular location (based on signal peptide and transmembrane predictions).
Stores raw and cleans expressed sequence tag (EST) classified in EST division of GenBank (dbEST) libraries. CleanEST is a web-based database server that provides two different cleansed sequences for each dbEST library: “pre-cleansed” and “user-cleansed”. The database uses an automatic user-cleansing pipeline, in which sequences in a user-selected library are cleansed on-the-fly according to user-input options. Four types of search menus are available: organism, sequencing center, eVOC ontologies (for human libraries) and user sequences.
Furnishes pig gene annotations in all sequenced genomic regions. PigGIS gathers 3.84 million whole genome shotgun (WGS) records generated by the Sino–Danish Pig Genome Project, 870 084 expressed sequence tags (ESTs) from 100 differentiated pig tissues/developmental stages, and 589 996 genomic reads together with 570 773 mRNA sequences extracted from GenBank.
Provides Physcomitrella patens DNA sequences. PHYSCObase is an online resource that gathers full-length enriched cDNA libraries of P. patens from auxin- and cytokinin-treated gametophytes, as well as from gametophytes that were grown without exogenous plant hormones. These data are deposited in public databases together with the expressed sequence tag (EST) project.